Unverified Commit f5d8417d authored by Richard Berger's avatar Richard Berger
Browse files

Update pair tersoff zbl

parent c0324e55

src/MANYBODY/pair_tersoff_zbl.cpp

+92 −135
Original line number Diff line number Diff line
@@ -30,12 +30,13 @@ 
#include "math_const.h"

#include "math_special.h"

#include "utils.h"

#include "tokenizer.h"

#include "potential_file_reader.h"



using namespace LAMMPS_NS;

using namespace MathConst;

using namespace MathSpecial;



#define MAXLINE 1024

#define DELTA 4



/* ---------------------------------------------------------------------- */
@@ -63,93 +64,40 @@ PairTersoffZBL::PairTersoffZBL(LAMMPS *lmp) : PairTersoff(lmp) 


void PairTersoffZBL::read_file(char *file)

{

  int params_per_line = 21;

  char **words = new char*[params_per_line+1];



  memory->sfree(params);

  params = NULL;

  params = nullptr;

  nparams = maxparam = 0;



  // open file on proc 0



  FILE *fp;

  if (comm->me == 0) {

    fp = force->open_potential(file);

    if (fp == NULL) {

      char str[128];

      snprintf(str,128,"Cannot open Tersoff potential file %s",file);

      error->one(FLERR,str);

    }

  }



  // read each line out of file, skipping blank lines or leading '#'

  // store line of params if all 3 element tags are in element list



  int n,nwords,ielement,jelement,kelement;

  char line[MAXLINE],*ptr;

  int eof = 0;



  while (1) {

    if (comm->me == 0) {

      ptr = fgets(line,MAXLINE,fp);

      if (ptr == NULL) {

        eof = 1;

        fclose(fp);

      } else n = strlen(line) + 1;

    }

    MPI_Bcast(&eof,1,MPI_INT,0,world);

    if (eof) break;

    MPI_Bcast(&n,1,MPI_INT,0,world);

    MPI_Bcast(line,n,MPI_CHAR,0,world);



    // strip comment, skip line if blank



    if ((ptr = strchr(line,'#'))) *ptr = '\0';

    nwords = utils::count_words(line);

    if (nwords == 0) continue;



    // concatenate additional lines until have params_per_line words



    while (nwords < params_per_line) {

      n = strlen(line);

  if (comm->me == 0) {

        ptr = fgets(&line[n],MAXLINE-n,fp);

        if (ptr == NULL) {

          eof = 1;

          fclose(fp);

        } else n = strlen(line) + 1;

      }

      MPI_Bcast(&eof,1,MPI_INT,0,world);

      if (eof) break;

      MPI_Bcast(&n,1,MPI_INT,0,world);

      MPI_Bcast(line,n,MPI_CHAR,0,world);

      if ((ptr = strchr(line,'#'))) *ptr = '\0';

      nwords = utils::count_words(line);

    }

    PotentialFileReader reader(lmp, file, "Tersoff");

    char * line;



    if (nwords != params_per_line)

      error->all(FLERR,"Incorrect format in Tersoff potential file");

    while(line = reader.next_line(NPARAMS_PER_LINE)) {

      try {

        ValueTokenizer values(line, " \t\n\r\f");



    // words = ptrs to all words in line



    nwords = 0;

    words[nwords++] = strtok(line," \t\n\r\f");

    while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;

        std::string iname = values.next_string();

        std::string jname = values.next_string();

        std::string kname = values.next_string();



        // ielement,jelement,kelement = 1st args

        // if all 3 args are in element list, then parse this line

    // else skip to next line

        // else skip to next entry in file

        int ielement, jelement, kelement;



        for (ielement = 0; ielement < nelements; ielement++)

      if (strcmp(words[0],elements[ielement]) == 0) break;

          if (iname == elements[ielement]) break;

        if (ielement == nelements) continue;

        for (jelement = 0; jelement < nelements; jelement++)

      if (strcmp(words[1],elements[jelement]) == 0) break;

          if (jname == elements[jelement]) break;

        if (jelement == nelements) continue;

        for (kelement = 0; kelement < nelements; kelement++)

      if (strcmp(words[2],elements[kelement]) == 0) break;

          if (kname == elements[kelement]) break;

        if (kelement == nelements) continue;





        // load up parameter settings and error check their values



        if (nparams == maxparam) {
@@ -161,29 +109,30 @@ void PairTersoffZBL::read_file(char *file) 
        params[nparams].ielement = ielement;

        params[nparams].jelement = jelement;

        params[nparams].kelement = kelement;

    params[nparams].powerm = atof(words[3]);

    params[nparams].gamma = atof(words[4]);

    params[nparams].lam3 = atof(words[5]);

    params[nparams].c = atof(words[6]);

    params[nparams].d = atof(words[7]);

    params[nparams].h = atof(words[8]);

    params[nparams].powern = atof(words[9]);

    params[nparams].beta = atof(words[10]);

    params[nparams].lam2 = atof(words[11]);

    params[nparams].bigb = atof(words[12]);

    params[nparams].bigr = atof(words[13]);

    params[nparams].bigd = atof(words[14]);

    params[nparams].lam1 = atof(words[15]);

    params[nparams].biga = atof(words[16]);

    params[nparams].Z_i = atof(words[17]);

    params[nparams].Z_j = atof(words[18]);

    params[nparams].ZBLcut = atof(words[19]);

    params[nparams].ZBLexpscale = atof(words[20]);



    // currently only allow m exponent of 1 or 3



        params[nparams].powerm      = values.next_double();

        params[nparams].gamma       = values.next_double();

        params[nparams].lam3        = values.next_double();

        params[nparams].c           = values.next_double();

        params[nparams].d           = values.next_double();

        params[nparams].h           = values.next_double();

        params[nparams].powern      = values.next_double();

        params[nparams].beta        = values.next_double();

        params[nparams].lam2        = values.next_double();

        params[nparams].bigb        = values.next_double();

        params[nparams].bigr        = values.next_double();

        params[nparams].bigd        = values.next_double();

        params[nparams].lam1        = values.next_double();

        params[nparams].biga        = values.next_double();

        params[nparams].Z_i         = values.next_double();

        params[nparams].Z_j         = values.next_double();

        params[nparams].ZBLcut      = values.next_double();

        params[nparams].ZBLexpscale = values.next_double();

        params[nparams].powermint = int(params[nparams].powerm);

      } catch (TokenizerException & e) {

        error->one(FLERR, e.what());

      }



      // currently only allow m exponent of 1 or 3

      if (params[nparams].c < 0.0 ||

          params[nparams].d < 0.0 ||

          params[nparams].powern < 0.0 ||
@@ -207,8 +156,16 @@ void PairTersoffZBL::read_file(char *file) 


      nparams++;

    }

  }



  MPI_Bcast(&nparams, 1, MPI_INT, 0, world);

  MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);



  if(comm->me != 0) {

    params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params");

  }



  delete [] words;

  MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world);

}



/* ---------------------------------------------------------------------- */

src/MANYBODY/pair_tersoff_zbl.h

+2 −0
Original line number Diff line number Diff line
@@ -29,6 +29,8 @@ class PairTersoffZBL : public PairTersoff { 
  PairTersoffZBL(class LAMMPS *);

  ~PairTersoffZBL() {}



  static const int NPARAMS_PER_LINE = 21;



 protected:

  double global_a_0;                // Bohr radius for Coulomb repulsion

  double global_epsilon_0;        // permittivity of vacuum for Coulomb repulsion

unittest/formats/test_potential_file_reader.cpp

+11 −0
Original line number Diff line number Diff line
@@ -9,6 +9,7 @@ 
#include "MANYBODY/pair_tersoff.h"

#include "MANYBODY/pair_tersoff_mod.h"

#include "MANYBODY/pair_tersoff_mod_c.h"

#include "MANYBODY/pair_tersoff_zbl.h"



#include <mpi.h>
@@ -20,6 +21,7 @@ const int LAMMPS_NS::PairComb3::NPARAMS_PER_LINE; 
const int LAMMPS_NS::PairTersoff::NPARAMS_PER_LINE;

const int LAMMPS_NS::PairTersoffMOD::NPARAMS_PER_LINE;

const int LAMMPS_NS::PairTersoffMODC::NPARAMS_PER_LINE;

const int LAMMPS_NS::PairTersoffZBL::NPARAMS_PER_LINE;



class PotenialFileReaderTest : public ::testing::Test {

protected:
@@ -95,6 +97,15 @@ TEST_F(PotenialFileReaderTest, TersoffModC) { 
    ASSERT_EQ(utils::count_words(line), PairTersoffMODC::NPARAMS_PER_LINE);

}



TEST_F(PotenialFileReaderTest, TersoffZBL) {

    ::testing::internal::CaptureStdout();

    PotentialFileReader reader(lmp, "SiC.tersoff.zbl", "Tersoff");

    ::testing::internal::GetCapturedStdout();



    auto line = reader.next_line(PairTersoffZBL::NPARAMS_PER_LINE);

    ASSERT_EQ(utils::count_words(line), PairTersoffZBL::NPARAMS_PER_LINE);

}



int main(int argc, char **argv)

{

    MPI_Init(&argc, &argv);

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